Insulin-like growth factor II (IGF-II) is a crucial factor in regulating cell proliferation, growth, migration, differentiation and survival. The objective of this study was to investigate the association of polymorphism in intron 3 and exon 3 of insulin like growth factor II (IGF-II) gene and body weight trait in tilapia nilotica fish using restriction fragment length polymorphism (RFLP) and single nucleotide polymorphism (SNP) techniques. Thirty tilapia nilotica fish were precisely selected according to their body weight and ordered from the largest to the smallest body size. DNA was extracted from fish blood samples to amplify 397-bp of IGF-II gene. Amplified IGF-II gene was sequenced only in the seven large and five small size fish. Results revealed that restriction analysis (RFLP) with MSP1 of the (IGF-II) gene (397-bp) do not produce restriction fragments. While, DNA sequencing showed fourteen single nucleotide polymorphisms (SNP's) at different positions in large size fish as they were detected in more than one fish at nucleotides number 318 (C→T), 319 (A→T), 320 (G→A in three fish), 322 (C→A and C→G), 323 (G→C and G→A), 326 (G→A in three fish), 332 (A→T in three fish), 333 (C→A and C→T), 334 (A→C in two fish), 337 (C→T in two fish) and 340 (C→T). Hence, our results reveal the possibility to use these findings as marker for selection of high body weight trait in tilapia nilotica fish.